Changed the default value for the wild type (namely, NA values) from 0.0 to 2.0.

gemme.py

@@ -146,7 +146,7 @@ def parseGEMMEoutput(inputFile, verbose):
             if item[0] == "\"":
                 aaColumn.append(item)
             elif (item == 'NA'):
-                tempList.append(0.0000000)
+                tempList.append(2.0000000)
             else:
                 tempList.append(float(item))
         matrixData.append(tempList)

pred.R

@@ -362,7 +362,7 @@ computePredSimple<-function(mat, distTrace, wt, thresh){
           if((i==694) & (a=="v")) {
             print(i)
             print(sel)
-            #print(distTrace[sel-1])
+            print(distTrace[sel-1])
             print(sortedDist)
             }
           
@@ -393,6 +393,8 @@ normalizePred<-function(pred, trace, wt){
 		normPred[,i] = pred[,i] / max(pred[!is.na(pred)])
 		normPred[is.na(normPred[,i]),i] = 1
 		normPred[,i] = normPred[,i] * trace[i]
+    # If the residue is the wild type, it is replaced by NA. 
+    # As explained above, NA corresponds to 2. 
 		normPred[aa==wt[i],i] = NA
 	}
 	return(-normPred)